Is Cysteine polar or nonpolar? - Polarity of Cysteine

The importance of amino acids is unparalleled in the human body. Amino acids are the building blocks of proteins, the workhorses of life.

There are 20 different types of naturally present amino acids. These amino acids are further classified into essential and non-essential, charged and neutral, polar and non-polar amino acids, etc.

Cysteine is a non-essential amino acid that our body can self-synthesize. Its primary function is to stabilize the three-dimensional shape and structure of a protein by forming strong, disulfide linkages.

In this article, we will find out whether cysteine is a polar or a non-polar amino acid and the reason behind it. So, let’s begin!

Is cysteine polar or non-polar?

Cysteine (C₃H₇NO₂S) is a polar amino acid.

The polarity of an amino acid largely depends on the side chain attached to the alpha carbon. A polar, sulfur-containing thiol (-SH) functional group is present in the side chain of cysteine, so it is overall polar.

The covalent bonds present in the carboxylic acid, amino, and thiol groups of cysteine are individually strongly polar as per a high electronegativity difference between the bonded atoms.

The charged electron cloud stays non-uniformly spread over the amino acid as the unequal dipole moments of the COOH, NH_2, and SH functional groups stay uncancelled to yield an overall polar cysteine molecule.

Now before proceeding further, let us first discuss the chemical structure of cysteine in detail.

What is the chemical structure of cysteine?

The general structure of an amino acid comprises a carbon (C) atom at the center, known as alpha carbon. It is covalently bonded to a carboxylic acid (COOH) group on one side and an amino (NH₂) group on the other side. A side chain (R) is attached at the third end, followed by a single H-atom at the fourth end, completing the structure of the amino acid.

The different amino acids are distinguished from each other based on the different side chains attached. A CH₂-SH group is attached as the side chain in cysteine.

The chemical structure of cysteine is shown below.

The five main types of elemental atoms present in a cysteine molecule are carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and sulfur (S).

All the H-atoms have a complete duplet in the above structure, while the other atoms complete their octets.

All 4 valence electrons of the central C-atom get consumed in covalent bonding; thus, there is no lone pair on this atom.

In contrast, 2 lone pairs of electrons are present on each of the two O-atoms and the S-atom. Conversely, 1 lone pair of electrons is present on the N-atom, respectively.

In a liquid medium such as a biological cell, a cysteine molecule may lose or gain a proton (H⁺ ion) and convert into charged species, depending upon the pH of the solution.

At the isoelectric point, both the acidic (COOH) and basic (NH₂) functional groups of the cysteine molecule get ionized.

+1 formal charge cancels with -1, forming a zwitterion; thus, cysteine acts as an uncharged/neutral amino acid.  

What makes a molecule polar or non-polar?

A molecule is polar if there is a non-uniform charge distribution present in it. If the charge distribution gets equally balanced in different parts, then that molecule is considered non-polar.

The following three factors mainly influence the polarity of a molecule:

• The electronegativity difference between two or more covalently bonded atoms
• Dipole moment
• Molecular geometry or shape

Now let’s see how the above three factors make cysteine a polar molecule overall.

Factors affecting the polarity of cysteine

Electronegativity

It is defined as the ability of an elemental atom to attract a shared pair of electrons from a covalent chemical bond.

Electronegativity increases across a period in the Periodic Table while it decreases down the group.

Greater the electronegativity difference between bonded atoms in a molecule, the higher the bond polarity.

Let’s break down the structure of cysteine based on the multiple different bonds present in it.

In the cysteine molecule, there are 2 C-C bonds, 3 C-H bonds, 1 C-O bond, 1 C=O bond, 1 C-N bond, 2 N-H bonds, 1 C-S bond, 1 S-H bond and 1 O-H bond.

The C-C single covalent bonds are purely non-polar, formed between two identical carbon atoms with zero or no electronegativity differences.

Similarly, the C-S bond is non-polar as a negligible electronegativity difference of 0.03 units exists between a carbon and a sulfur atom.

The S-H and C-H bonds are slightly polar as per the small electronegativity differences of 0.38 units and 0.35 units between the bonded atoms, respectively.

It is less than 0.4 units required for a covalent chemical bond to be polar as per Pauling’s electronegativity scale. But still, as it is formed between two dissimilar atoms, so the slightly more electronegative atom (S or C) gains a partial negative charge (δ^–), while the corresponding H-atoms attain partial positive charges (δ⁺).

In contrast, the C-O (or C=O) and O-H bonds present in the carboxylic acid (COOH) group are strongly polar, possessing high electronegativity differences of 0.89 units and 1.24 units between the bonded atoms.

Oxygen, being strongly electronegative, attracts the shared electron cloud largely towards itself, and oppositely charged poles develop in the molecule. 

Finally, the C-N and N-H bonds present in cysteine are also polar owing to the specific electronegativity differences of 0.49 units and 0.84 units between the covalently bonded atoms, respectively.

Dipole moment

Dipole moment (μ) is a vector quantity that points from the positive pole to the negative pole of a bond or a molecule.

It is mathematically calculated as a product of the magnitude of charge (Q) and charge separation (r). The dipole moment is expressed in a unit called Debye (D).

The dipole moment of a polar covalent bond conventionally points from the positive center to the center of the negative charge.

In the cysteine molecule, the S-H dipole moment in the side chain points from S^δ– to H^δ+. Similarly, the strong dipole moments of polar bonds present in COOH and NH₂ functional groups are directed, as shown below.

Molecular geometry

According to the valence shell electron pair repulsion (VSEPR) theory of chemical bonding, cysteine is an AX₄-type molecule w.r.t the central alpha C-atom. To one carbon atom at the center (C), four different bond pairs (X) are attached, and there is no lone pair of electrons (E) present on it. So cysteine is a tetrahedral molecule w.r.t the central C-atom.

Contrarily, the molecular shape of cysteine w.r.t the S-atom and O-atoms containing 2 lone pairs each is bent, angular or V-shaped.

In either case, the dipole moments of the individually polar bonds (esp. the S-H bond) stay uncancelled to yield an overall polar cysteine molecule with a permanent dipole moment value.

An important point for you to note is that free cysteine is polar.

However, cysteine uses its –SH group to form strong disulfide linkages with other cysteine residues in a protein molecule. This results in an oxidized derivative of cysteine called cystine.

Cystine is essentially non-polar in nature and dissolves poorly in polar solvents such as water, as the S-H bonds are replaced by S-S bonds possessing zero electronegativity differences.

Thus, cysteine in bound form is non-polar.

FAQ

Summary

• Cysteine (C₃H₇NO₂S) is a polar amino acid.
• It consists of polar C-O (or C=O), O-H, C-N, N-H, and S-H bonds possessing specific electronegativity differences.
• The dipole moments of the polar bonds present in cysteine stay uncancelled due to the asymmetric bent shape of the amino acid w.r.t the S-atom in the side chain and the O-atoms.
• The charged electron cloud stays unsymmetrically spread over the molecule, yielding an overall polar amino acid with a permanent dipole moment value (net µ > 0).

References

1. Unacademy. ‘A short note on polar amino acids’’. https://unacademy.com/content/upsc/study-material/chemistry/a-short-note-on-polar-amino-acids/
2. Khan Academy. ‘Classification of amino acids.’’ https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/classification-amino-acid
3. AK Lectures. ‘Nonpolar and uncharged polar amino acids’’. https://aklectures.com/lecture/structure-of-proteins/nonpolar-and-uncharged-polar-amino-acids
4. Wikipedia. The Free Encyclopedia. ‘Cysteine’’. https://en.wikipedia.org/wiki/Cysteine
5. Amino Science. ‘What are nonpolar amino acids?’’. March 6^th, 2019. https://aminoco.com/blogs/amino-acids/what-are-non-polar-amino-acids